Merging Taxonomy with Ecological Population Prediction in a Case Study of Vibrionaceae

Abstract

We synthesized population structure data from three studies that assessed the fine-scale distribution of Vibrionaceae among temporally and spatially distinct environmental categories in coastal seawater and animals. All studies used a dynamic model (AdaptML) to identify phylogenetically cohesive and ecologically distinct bacterial populations and their predicted habitats without relying on a predefined genetic cutoff or relationships to previously named species. Across the three studies, populations were highly overlapping, displaying similar phylogenetic characteristics (identity and diversity), and were predominantly congruent with taxonomic Vibrio species previously characterized as genotypic clusters by multilocus sequence analysis (MLSA). The environmental fidelity of these populations appears high, with 9 out of 12 reproducibly associating with the same predicted (micro)habitats when similar environmental categories were sampled. Overall, this meta-analysis provides information on the habitat predictability and structure of previously described species, demonstrating that MLSA-based taxonomy can, at least in some cases, serve to approximate ecologically cohesive populations.

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton

“…Two deep-branching clusters were grouped into a single population by AdaptML, but were treated separately (populations #1 and #2) because of their distinct phylogeny and the fact that #1 was overlapping between years, whereas #2 was observed in 2006 only. We also note that, previously, populations #6, #9, #11 and #14 were listed as members of V. splendidus (Hunt et al, 2008a); however, since then taxonomic revision of populations predicted in our studies has shown that only population #9 is congruent with V. splendidus (though we note that there is disagreement among taxonomists; Le Roux et al, 2009;Preheim et al, 2011b;Supplementary Table 1).…”

“…Sampling during different seasons has revealed strong temporal differentiation with the same 'habitat' type often occupied by season-specific populations (Hunt et al, 2008a;Preheim et al, 2011a). Moreover, two studies carried out 1 year apart but targeting different types of samples from coastal water have suggested population re-occurrence (Preheim et al, 2011b); however, the evidence remains indirect since no sampling scheme has been reproduced in a manner to ascertain to what extent populations occupy the same 'habitats'.…”

“…Hsp60 sequences were assigned to populations identified in 2006 based on multilocus sequence analysis as described in Preheim et al (2011b) and Supplementary Table 1. Taxonomic placement of unassigned populations was done by phylogenetic analysis of 16S rRNA gene sequences.…”

Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification

“…Thus MLSA provides significantly higher resolution. Similar considerations may be obtained from the investigations on the marine planktic genera Synechococcus and Prochlorococcus (Johnson et al 2006) or fine-scale distribution of marine Vibrionaceae (Preheim et al 2011). On the other hand, Kopac et al (2014) analyzed all orthologous genes within Bacillus subtilis and showed that MLSA was insufficient to distinguish ecotypes, which are considered as species in this paper.…”

Shape and evolution of the fundamental niche in marine Vibrio

“…MED222, V. parahaemolyticus, and V. fischeri MJ11, and L. anguillarum were obtained from complete genomes available on GenBank. For all other strains, partial sequences were obtained during previous studies using multilocus sequencing (Boucher et al, 2011;Preheim et al, 2011, and references therein). Sequences were aligned using MUSCLE (Edgar, 2004), and manually trimmed before concatenating all alignments.…”